The precedence for the USE setting is, ordered by priority (first has lowest priority):

Default USE setting declared in the make.defaults files part of your profile
User-defined USE setting in /etc/portage/make.conf
User-defined USE setting in /etc/portage/package.use
User-defined USE setting as environment variable

I did this entry in /etc/portage/package.use to point out that the configurations in /etc/make.conf don't produce any effect.

According to Gentoo Docs (as bogumillaska commented and I thought):

Quote:

The precedence for the USE setting is, ordered by priority (first has lowest priority):

Default USE setting declared in the make.defaults files part of your profile
User-defined USE setting in /etc/portage/make.conf
User-defined USE setting in /etc/portage/package.use
User-defined USE setting as environment variable

lighttpd should have been build without ipv6 because I disabled it in /etc/make.conf and didn't enable it again - neither in /etc/portage/package.use nor in the environment variable. And also python should have been build with ipv6 disabled (because of the configuration in /etc/make.conf).